DNA synthesis via the automated solid-phase method, whereby the DNA fragment is built up by the sequential addition of activated nucleotides to a growing chain that is linked to an insoluble support, has provided for the synthesis of DNA chains of up to 100 nucleotides long at an approximate rate of 10 minutes per base. Such artificial DNA strands with known sequence, the single stranded probe DNA, have been used to find the complementary counterpart in DNA samples by hybridization. Above a certain temperature (T.sub.m) the DNA double helix "melts" to form two complementary single strands which recombine upon cooling. If a single strand from the sample has the complementary sequence to the probe DNA they can hybridize to form a double helix. Detection of the DNA hybridization process is important for the development of methods and compositions for DNA synthesis and detection of specific nucleic acid sequences (e.g., detection of mutations, pathogens, and particular alleles). One approach for detecting DNA hybridization utilizes a quartz crystal microbalance, which is a very sensitive device to measure mass changes in the nanogram regime (Okahata et al., J. Am. Chem. Soc. 114:8299 [1992]. Another method of detecting DNA hybridization at surfaces employed the electrogenerated chemiluminescence (ECL) by intercalating an ECL marker into the double helix of the sample-probe DNA tethered to a surface (Xu et al., J. Am. Chem. Soc. 117:2627 [1995]). However, both methods are rather sensitive to interferences, such as chemical, pH, temperature, etc., and require sophisticated equipment.
There has been an increasing interest in the field of DNA sensors due to the impact of such devices on diverse areas of medical, environmental, and biological applications. (See e.g., Fodor et al., Science 251:767-773 [1991]; Maeda et al., Anal. Sciences 8:83-34 [1992]; Sakurai et al., Anal. Chem. 64:1996-1997 [1992]; Okahata et al., J. Am. Chem. Soc. 114:8299-8300 [1992]; Xu et al., J. Am. Chem. Soc. 117:2627-2631 [1995]; and Wang et al., Anal. Chem. 68:2629-2634 [1996]). Besides pure sequencing applications, such DNA sensors could help detect infectious or inherited diseases, or as RNA sensors, aid in monitoring expression levels of specific metabolic pathways to determine environmental pollution. DNA hybridization between a synthetic oligodeoxynucleotide of known sequence and its complement in a given sample provides a powerful tool for the detection and sequencing of DNA and RNA. The hybridization event itself is usually monitored by introducing fluorescent markers and radioactive labels or by applying antibody assays and enzyme reactions to the specifically modified DNA (or RNA) pair, which generally requires labor intensive and time consuming multistep procedures.
Thus, there remains a need of analyte detectors that provide for DNA detection that can be visually monitored by the naked eye, thus, making any further detection procedures ancillary or unnecessary.